Working Results2
Kaushik Narasimhan
Sys.Date()
Summary Statistics
Species Information
## Species Mammal.Bird
## 1 agouti Mammal
## 2 brown four-eyed oppossum Mammal
## 3 Baudo guan Bird
## 4 crab eating racoon Mammal
## 5 choco toucan Bird
## 6 chestnut-mandibled toucan Bird
## 7 coati Mammal
## 8 collared peccary Mammal
## 9 Greater Tinamou Bird
## 10 kinkajou Mammal
## 11 oilbird Bird
## 12 opossum Mammal
## 13 paca Mammal
## 14 red brocket deer Mammal
## 15 Rose faced parrot Bird
## 16 rufous fronted wood-quail (Odontophorus erythrops) Bird
## 17 rodent spp. Mammal
## 18 rufous tree rat Mammal
## 19 Southern mealy parrot Bird
## 20 squirrel spp. Mammal
## 21 toucan spp. Bird
## 22 Tomes spiny rat Mammal
## 23 Umbrellabird Bird
## 24 Wood-rail Bird
## Func.group sightings ingestions removals nibbles detections
## 1 TD 260 0 44 70 15
## 2 TD 82 2 2 4 12
## 3 FD 20 2 4 2 5
## 4 TD 1 0 0 0 1
## 5 FD 272 99 142 3 14
## 6 FD 316 157 168 1 16
## 7 TD 458 2 0 175 11
## 8 TD 136 4 0 0 7
## 9 TD 8 0 0 0 2
## 10 TD 84 0 3 14 9
## 11 FD 73 0 36 0 7
## 12 TD 100 1 0 27 8
## 13 TD 416 0 31 73 10
## 14 TD 5 0 0 0 1
## 15 FD 2 0 0 0 2
## 16 TD 434 0 0 4 15
## 17 TD 1380 0 197 45 21
## 18 TD 5 0 0 1 1
## 19 FD 10 0 7 0 1
## 20 TD 675 0 249 109 20
## 21 FD 284 75 85 0 15
## 22 TD 136 0 24 1 6
## 23 FD 269 34 96 2 20
## 24 TD 127 0 0 7 10
Visualization of ht vs focal 50
Scatter plots using 50m
Scatter of Disperser visitation at 50m fruiting neighborhood
Correlation at each band
effect of height focal against visitation
## $vis.rate
##
## $FD.rate
##
## $TD.rate
PCA of all environmental variables
PCA of selected environmental variables
Constrained ordination
Models 50 m band
## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: poisson ( log )
## Formula: real.visitation ~ focalmonth..50 * Height + offset(lograte) +
## (1 + focalmonth..50 | Tree)
## Data: cam_data_NFM1tree
##
## AIC BIC logLik deviance df.resid
## 3794.0 3815.6 -1890.0 3780.0 154
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -8.5540 -2.5265 -0.5044 1.5826 30.3127
##
## Random effects:
## Groups Name Variance Std.Dev. Corr
## Tree (Intercept) 2.055 1.433
## focalmonth..50 1.286 1.134 -0.59
## Number of obs: 161, groups: Tree, 49
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -0.33897 0.22232 -1.525 0.1273
## focalmonth..50 0.51673 0.28594 1.807 0.0707 .
## Heightlow 0.85862 0.04317 19.889 < 2e-16 ***
## focalmonth..50:Heightlow -0.27907 0.03740 -7.462 8.5e-14 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) fc..50 Hghtlw
## fclmnth..50 -0.435
## Heightlow -0.154 0.070
## fclmn..50:H 0.094 -0.101 -0.625## chisq ratio rdf p
## 3111.07009 20.20175 154.00000 0.00000## Family: poisson ( log )
## Formula:
## real.visitation ~ focalmonth..50 * Height + offset(lograte) +
## (1 + focalmonth..50 | Tree)
## Zero inflation: ~1
## Data: cam_data_NFM1tree
##
## AIC BIC logLik deviance df.resid
## 3290.9 3315.6 -1637.5 3274.9 153
##
## Random effects:
##
## Conditional model:
## Groups Name Variance Std.Dev. Corr
## Tree (Intercept) 1.386 1.177
## focalmonth..50 1.358 1.165 -0.71
## Number of obs: 161, groups: Tree, 49
##
## Conditional model:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 0.04057 0.18868 0.215 0.8298
## focalmonth..50 0.51522 0.29571 1.742 0.0815 .
## Heightlow 0.72385 0.04371 16.561 < 2e-16 ***
## focalmonth..50:Heightlow -0.27524 0.03749 -7.341 2.12e-13 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Zero-inflation model:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -1.8986 0.2343 -8.103 5.37e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Family: nbinom2 ( log )
## Formula:
## real.visitation ~ focalmonth..50 * Height + offset(lograte) +
## (1 + focalmonth..50 | Tree)
## Zero inflation: ~1
## Data: cam_data_NFM1tree
##
## AIC BIC logLik deviance df.resid
## NA NA NA NA 152
##
## Random effects:
##
## Conditional model:
## Groups Name Variance Std.Dev. Corr
## Tree (Intercept) 0.50309 0.7093
## focalmonth..50 0.08312 0.2883 -1.00
## Number of obs: 161, groups: Tree, 49
##
## Overdispersion parameter for nbinom2 family (): 1.03
##
## Conditional model:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 0.3972 0.2541 1.563 0.11804
## focalmonth..50 0.2843 0.2257 1.260 0.20776
## Heightlow 0.8123 0.2476 3.281 0.00103 **
## focalmonth..50:Heightlow -0.3448 0.2154 -1.601 0.10935
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Zero-inflation model:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -2.3114 0.3876 -5.964 2.47e-09 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Conditional model:
## (Intercept) focalmonth..50
## 0.3972 0.2843
## Heightlow focalmonth..50:Heightlow
## 0.8123 -0.3448
##
## Zero-inflation model:
## (Intercept)
## -2.311## Family: nbinom2 ( log )
## Formula:
## real.visitation ~ focalmonth..50 * Height + offset(lograte) +
## (1 + focalmonth..50 | Tree)
## Data: cam_data_NFM1tree
##
## AIC BIC logLik deviance df.resid
## NA NA NA NA 153
##
## Random effects:
##
## Conditional model:
## Groups Name Variance Std.Dev. Corr
## Tree (Intercept) 0.38819 0.6231
## focalmonth..50 0.04484 0.2118 -1.00
## Number of obs: 161, groups: Tree, 49
##
## Overdispersion parameter for nbinom2 family (): 0.675
##
## Conditional model:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 0.2902 0.2547 1.139 0.25470
## focalmonth..50 0.2307 0.2351 0.981 0.32652
## Heightlow 0.9401 0.2697 3.486 0.00049 ***
## focalmonth..50:Heightlow -0.3388 0.2531 -1.338 0.18079
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: poisson ( log )
## Formula: real.visitation ~ focalmonth..50 * Height + offset(lograte) +
## (1 | obs_effect) + (1 + focalmonth..50 | Tree)
## Data: cam_data_NFM1tree
##
## AIC BIC logLik deviance df.resid
## 1454.6 1479.2 -719.3 1438.6 153
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.16823 -0.19820 0.02129 0.07651 0.31996
##
## Random effects:
## Groups Name Variance Std.Dev. Corr
## obs_effect (Intercept) 1.93269 1.3902
## Tree (Intercept) 0.71153 0.8435
## focalmonth..50 0.05528 0.2351 -1.00
## Number of obs: 161, groups: obs_effect, 161; Tree, 49
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -0.6735 0.2793 -2.411 0.0159 *
## focalmonth..50 0.1535 0.2008 0.765 0.4445
## Heightlow 1.2254 0.2929 4.183 2.87e-05 ***
## focalmonth..50:Heightlow -0.2117 0.2415 -0.876 0.3808
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) fc..50 Hghtlw
## fclmnth..50 -0.549
## Heightlow -0.705 0.422
## fclmn..50:H 0.360 -0.768 -0.533
## convergence code: 0
## boundary (singular) fit: see ?isSingular## [1] FALSE## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -0.339 0.999 -0.34 0.734
## focalmonth..50 0.517 1.285 0.40 0.688
## Heightlow 0.859 0.194 4.43 9.6e-06 ***
## focalmonth..50:Heightlow -0.279 0.168 -1.66 0.097 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1